Added if exists/select + drop statement for the i2b2concept synonym. …

…Added if exists/select + drop statements for the primary key constraints on the measurement, drug exposure, procedure occurrence and condition occurrence tables

MSSQL/OMOPLoader.sql

@@ -20,10 +20,11 @@
 ----------------------------------------------------------------------------------------------------------------------------------------
 
 -- Change to your omop database
-use PMI
+use i2b2stub;
 go
 
 -- drop any existing synonyms
+IF  EXISTS (SELECT * FROM sys.synonyms WHERE name = N'i2b2concept') DROP SYNONYM i2b2concept
 IF  EXISTS (SELECT * FROM sys.synonyms WHERE name = N'i2b2fact') DROP SYNONYM i2b2fact
 IF  EXISTS (SELECT * FROM sys.synonyms WHERE name = N'i2b2patient') DROP SYNONYM  i2b2patient
 IF  EXISTS (SELECT * FROM sys.synonyms WHERE name = N'i2b2visit') DROP SYNONYM  i2b2visit
@@ -41,31 +42,35 @@ GO
 
 -- You will almost certainly need to edit your database name
 -- Synonyms for dimension tables
-create synonym i2b2visit for PMI..visit_dimension
+create synonym i2b2visit for i2b2stub..visit_dimension
 GO 
-create synonym i2b2patient for  PMI..patient_dimension
+create synonym i2b2patient for  i2b2stub..patient_dimension
 GO
-create synonym i2b2fact for  PMI..observation_fact    
+create synonym i2b2fact for  i2b2stub..observation_fact    
 GO
-create synonym i2b2concept for  PMI..concept_dimension  
+create synonym i2b2concept for  i2b2stub..concept_dimension  
 GO
 
 -- You will almost certainly need to edit your database name
 -- Synonyms for ontology dimensions and loyalty cohort summary
-create synonym pcornet_med for PMI..pcornet_med
-GO
-create synonym pcornet_lab for PMI..pcornet_lab
-GO
-create synonym pcornet_diag for PMI..pcornet_diag
-GO 
-create synonym pcornet_demo for PMI..pcornet_demo 
-GO
-create synonym pcornet_proc for PMI..pcornet_proc
-GO
-create synonym pcornet_vital for PMI..pcornet_vital_30
-GO
-create synonym pcornet_enc for PMI..pcornet_enc_15
-GO
+-- The synonyms in comments have identical names to the tables - 
+-- you will only need to edit and uncomment if your tables have
+-- names other than these
+
+--create synonym pcornet_med for i2b2stub..pcornet_med
+--GO
+--create synonym pcornet_lab for i2b2stub..pcornet_lab
+--GO
+--create synonym pcornet_diag for i2b2stub..pcornet_diag
+--GO 
+--create synonym pcornet_demo for i2b2stub..pcornet_demo 
+--GO
+create synonym pcornet_proc for i2b2stub..pcornet_proc_nocpt
+GO
+--create synonym pcornet_vital for i2b2stub..pcornet_vital
+--GO
+--create synonym pcornet_enc for i2b2stub..pcornet_enc
+--GO
 
 -- Create the demographics codelist (no need to modify)
 IF  EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'[dbo].[omop_codelist]') AND type in (N'U'))
@@ -156,28 +161,40 @@ GO
 
 
 
-
+IF  EXISTS (SELECT * FROM INFORMATION_SCHEMA.TABLE_CONSTRAINTS WHERE CONSTRAINT_NAME = 'xpk_condition_occurrence') 
+	Alter table condition_occurrence DROP constraint xpk_condition_occurrence
+Go
 Alter Table condition_occurrence Drop Column condition_occurrence_id
 Go
 
 Alter Table condition_occurrence
 Add condition_occurrence_id Int Identity(1, 1)
 Go
 
+
+IF  EXISTS (SELECT * FROM INFORMATION_SCHEMA.TABLE_CONSTRAINTS WHERE CONSTRAINT_NAME = 'xpk_procedure_occurrence') 
+	Alter table procedure_occurrence DROP constraint xpk_procedure_occurrence
+Go
 Alter Table procedure_occurrence Drop Column procedure_occurrence_id
 Go
 
 Alter Table procedure_occurrence
 Add procedure_occurrence_id Int Identity(1, 1)
 Go
 
+IF  EXISTS (SELECT * FROM INFORMATION_SCHEMA.TABLE_CONSTRAINTS WHERE CONSTRAINT_NAME = 'xpk_measurement') 
+	Alter table measurement DROP constraint xpk_measurement
+Go
 Alter Table measurement Drop Column measurement_id
 Go
 
 Alter Table measurement
 Add measurement_id Int Identity(1, 1)
 Go
 
+IF  EXISTS (SELECT * FROM INFORMATION_SCHEMA.TABLE_CONSTRAINTS WHERE CONSTRAINT_NAME = 'xpk_drug_exposure') 
+	Alter table drug_exposure DROP constraint xpk_drug_exposure
+Go
 Alter Table drug_exposure Drop Column drug_exposure_id
 Go